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Élez E, Mulet-Margalef N, Sanso M, Ruiz-Pace F, Mancuso FM, Comas R, Ros J, Argilés G, Martini G, Sanz-Garcia E, Baraibar I, Salvà F, Noguerido A, Cuadra-Urteaga JL, Fasani R, Garcia A, Jimenez J, Aguilar S, Landolfi S, Hernández-Losa J, Braña I, Nuciforo P, Dienstmann R, Tabernero J, Salazar R, Vivancos A. A Comprehensive Biomarker Analysis of Microsatellite Unstable/Mismatch Repair Deficient Colorectal Cancer Cohort Treated with Immunotherapy. Int J Mol Sci 2022; 24:ijms24010118. [PMID: 36613564 PMCID: PMC9820517 DOI: 10.3390/ijms24010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The search for immunotherapy biomarkers in Microsatellite Instability High/Deficient Mismatch Repair system (MSI-H/dMMR) metastatic colorectal cancer (mCRC) is an unmet need. Sixteen patients with mCRC and MSI-H/dMMR (determined by either immunohistochemistry or polymerase chain reaction) treated with PD-1/PD-L1 inhibitors at our institution were included. According to whether the progression-free survival with PD-1/PD-L1 inhibitors was longer than 6 months or shorter, patients were clustered into the IT-responder group (n: 9 patients) or IT-resistant group (n: 7 patients), respectively. In order to evaluate determinants of benefit with PD-1/PD-L1 inhibitors, we performed multimodal analysis including genomics (through NGS panel tumour-only with 431 genes) and the immune microenvironment (using CD3, CD8, FOXP3 and PD-L1 antibodies). The following mutations were more frequent in IT-resistant compared with IT-responder groups: B2M (4/7 versus 2/9), CTNNB1 (2/7 versus 0/9), and biallelic PTEN (3/7 versus 1/9). Biallelic ARID1A mutations were found exclusively in the IT-responder group (4/9 patients). Tumour mutational burden did not correlate with immunotherapy benefit, neither the rate of indels in homopolymeric regions. Of note, biallelic ARID1A mutated tumours had the highest immune infiltration and PD-L1 scores, contrary to tumours with CTNNB1 mutation. Immune microenvironment analysis showed higher densities of different T cell subpopulations and PD-L1 expression in IT-responders. Misdiagnosis of MSI-H/dMMR inferred by discordances between immunohistochemistry and polymerase chain reaction was only found in the IT-resistant population (3/7 patients). Biallelic ARID1A mutations and Wnt signalling activation through CTNNB1 mutation were associated with high and low T cell immune infiltrates, respectively, and deserve special attention as determinants of response to PD-1/PD-L1 inhibitors. The non-MSI-H phenotype in dMMR is associated with poor benefit to immunotherapy. Our results suggest that mechanisms of resistance to immunotherapy are multi-factorial.
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Affiliation(s)
- Elena Élez
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Núria Mulet-Margalef
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
- Colorectal Cancer Unit, Medical Oncology Department, Catalan Institute of Oncology, L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Miriam Sanso
- Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
- Genomics for Precision Oncology Laboratory, Fundació Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Fiorella Ruiz-Pace
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Francesco M. Mancuso
- Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
- Research and Development Department, Universal Diagnostics S.L., 41013 Sevilla, Spain
| | - Raquel Comas
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Javier Ros
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
- Departament of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 81100 Naples, Italy
| | - Guillem Argilés
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Giulia Martini
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
- Departament of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, 81100 Naples, Italy
| | - Enrique Sanz-Garcia
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Iosune Baraibar
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Francesc Salvà
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Alba Noguerido
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Jose Luis Cuadra-Urteaga
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
- Medical Oncology, IOB—Hospital Quirón, 08023 Barcelona, Spain
| | - Roberta Fasani
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Ariadna Garcia
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Jose Jimenez
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Susana Aguilar
- Molecular Prescreening Program, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Stefania Landolfi
- Department of Pathology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain
| | | | - Irene Braña
- Medical Oncology Department, Research Unit for Molecular Therapy of Cancer, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Josep Tabernero
- Colorectal Cancer Program, Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Ramon Salazar
- Colorectal Cancer Unit, Medical Oncology Department, Catalan Institute of Oncology, L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Medical Oncology Department, Catalan Institute of Oncology, Oncobell Program (IDIBELL), CIBERONC, L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
- Correspondence: ; Tel.: +34-932-543-450
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2
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Frigola J, Navarro A, Carbonell C, Callejo A, Iranzo P, Cedrés S, Martinez‐Marti A, Pardo N, Saoudi‐Gonzalez N, Martinez D, Jimenez J, Sansano I, Mancuso FM, Nuciforo P, Montuenga LM, Sánchez‐Cespedes M, Prat A, Vivancos A, Felip E, Amat R. Molecular profiling of long-term responders to immune checkpoint inhibitors in advanced non-small cell lung cancer. Mol Oncol 2021; 15:887-900. [PMID: 33342055 PMCID: PMC8024716 DOI: 10.1002/1878-0261.12891] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Immunotherapy has transformed advanced non-small cell lung cancer (NSCLC) treatment strategies and has led to unprecedented long-lasting responses in some patients. However, the molecular determinants driving these long-term responses remain elusive. To address this issue, we performed an integrative analysis of genomic and transcriptomic features of long-term immune checkpoint inhibitors (ICIs)-associated responders. We assembled a cohort of 47 patients with NSCLC receiving ICIs that was enriched in long-term responders [>18 months of progression-free survival (PFS)]. We performed whole-exome sequencing from tumor samples, estimated the tumor mutational burden (TMB), and inferred the somatic copy number alterations (SCNAs). We also obtained gene transcription data for a subset of patients using Nanostring, which we used to assess the tumor immune infiltration status and PD-L1 expression. Our results indicate that there is an association between TMB and benefit to ICIs, which is driven by those patients with long-term response. Additionally, high SCNAs burden is associated with poor response and negatively correlates with the presence of several immune cell types (B cells, natural killers, regulatory T cells or effector CD8 T cells). Also, CD274 (PD-L1) expression is increased in patients with benefit, mainly in those with long-term response. In our cohort, combined assessment of TMB and SCNAs burden enabled identification of long-term responders (considering PFS and overall survival). Notably, the association between TMB, SCNAs burden, and PD-L1 expression with the outcomes of ICIs treatment was validated in two public datasets of ICI-treated patients with NSCLC. Thus, our data indicate that TMB is associated with long-term benefit following ICIs treatment in NSCLC and that TMB, SCNAs burden, and PD-L1 are complementary determinants of response to ICIs.
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Affiliation(s)
- Joan Frigola
- Thoracic Cancers Translational Genomics UnitHebron Institute of Oncology (VHIO)Vall dBarcelonaSpain
| | - Alejandro Navarro
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Caterina Carbonell
- Thoracic Cancers Translational Genomics UnitHebron Institute of Oncology (VHIO)Vall dBarcelonaSpain
| | - Ana Callejo
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Patricia Iranzo
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Susana Cedrés
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Alex Martinez‐Marti
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Nuria Pardo
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Nadia Saoudi‐Gonzalez
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Debora Martinez
- Department of Medical OncologyHospital ClinicBarcelonaSpain
- Translational Genomics and Targeted Therapies in Solid TumorsIDIBAPSBarcelonaSpain
| | - Jose Jimenez
- Molecular Oncology GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Irene Sansano
- Pathology UnitVall d’Hebron University HospitalBarcelonaSpain
| | - Francesco M. Mancuso
- Cancer Genomics LaboratoryVall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Paolo Nuciforo
- Molecular Oncology GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Luis M. Montuenga
- Program in Solid TumorsCenter for Applied Medical Research (CIMA)PamplonaSpain
- Department of Pathology, Anatomy and PhysiologySchool of MedicineUniversity of NavarraPamplonaSpain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)MadridSpain
- Navarra Health Research Institute (IDISNA)PamplonaSpain
| | - Montse Sánchez‐Cespedes
- Cancer Genetics GroupJosep Carreras Leukaemia Research Institute (IJC)Campus ICO‐Germans Trias i PujolBadalona, BarcelonaSpain
| | - Aleix Prat
- Department of Medical OncologyHospital ClinicBarcelonaSpain
- Translational Genomics and Targeted Therapies in Solid TumorsIDIBAPSBarcelonaSpain
| | - Ana Vivancos
- Cancer Genomics LaboratoryVall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Enriqueta Felip
- Thoracic Cancers Translational Genomics UnitHebron Institute of Oncology (VHIO)Vall dBarcelonaSpain
- Oncology DepartmentVall d’Hebron University Hospital & Vall d’Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | - Ramon Amat
- Thoracic Cancers Translational Genomics UnitHebron Institute of Oncology (VHIO)Vall dBarcelonaSpain
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3
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Martini G, Elez E, Mancuso FM, Gomez MA, Caratu G, Matito J, Argiles G, Mulet N, Baraibar I, Ros J, Garcia A, Comas R, Ligero M, Santos C, Nuciforo P, Dienstmann R, Tabernero J, Aranda E, Perez-Lopez R, Vivancos A. The predictive role of plasma mutant allele fraction to antiangiogenic drugs in patients with mCRC: An expanded analysis of surrogate biomarkers of response to first-line treatment with bevacizumab. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3541 Background: So far, no biomarkers of response to anti-angiogenic drugs are available in colorectal cancer (CRC) treatment. Liquid biopsy tracks dynamic mutational changes in CRC patients (pts). RAS mutant allele fraction in plasma (plMAF) is an independent prognostic marker in metastatic CRC (mCRC). We explored the predictive value of plMAF in RAS mutant pts treated in 1st line with chemotherapy +/- bevacizumab (bev). Methods: A multicentric prospective/retrospective analysis was conducted. We collected data from 226 mCRC pts and selected the subset not eligible for metastasis resection with basal plMAF sample evaluable for RAS mutant MAF quantification with digital PCR (BEAMing). Pts were stratified as high (≥ 5.8%) or low ( < 5.8%) plMAF. We investigated associations between clinicopathological variables and progression-free survival (PFS) stratified by plMAF RAS levels using Cox regression models and survival data were calculated by Kaplan-Meier method. Computational analysis of baseline CT scan data extracted 93 radiomics features of all the lesions per patient including 1) 1st class from density histogram distribution and texture analysis by 2) 2nd order and 3) higher order feature classes. The radiomic features distribution between pts with high and low pIMAF was assessed with Student’s t-test analysis. Results: From October 17 to May 19, 63 basal plasma samples were analysed with BEAMing. 42 pts (67.7%) were classified as high and 21 pts (32,3%) as low plMAF. In high plMAF subgroup, a statistically significant longer PFS favouring FOLFOX+bev was observed, compared to FOLFOX alone (10.7 vs 6.9 mts; HR: 0.30; p = 0.002). In low RAS plMAF subgroup, no differences in terms of PFS were observed in either arm (8.9 vs 8.7 mts; HR: 0.7; p = 0.6). Multivariate PFS model showed no association between RAS plMAF and clinicopathological variables, except for high RAS plMAF and treatment benefit with FOLFOX+bev. The CT-radiomics signature, that may translate tumor vascularization, differentiated patients with high vs low pIMAF (p = 0.002). 58 patients (92%) had similar radiomic score; 5 patients with high plMAF (8%) presented very heterogeneous radiomic score distribution. Conclusions: Tumor-borne RAS plMAFs may constitute a potential predictive biomarker of efficacy for anti-angiogenic drugs in mCRC. Next steps will include the identification of -histological, transcriptomic and radiomic- surrogate biomarkers of response that reflect tumor irrigational status.
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Affiliation(s)
- Giulia Martini
- Medical Oncology, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Elena Elez
- Medical Oncology Department, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Ginevra Caratu
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Guillem Argiles
- Vall d’Hebron University Hospital and Institute of Oncology (VHIO), CIBERONC, TTD Group, Barcelona, Spain
| | - Nuria Mulet
- Instituto Catalan de Oncologia de Hospitalet, Barcelona, Spain
| | - Iosune Baraibar
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Javier Ros
- Medical Oncology Department, Vall d´Hebron University Hospital/Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ariadna Garcia
- Medical Oncology Department, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Raquel Comas
- Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Ligero
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Cristina Santos
- Translational Research Laboratory and Department of Medical Oncology, Institut Català d'Oncologia-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Josep Tabernero
- Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Enrique Aranda
- IMIBIC, Reina Sofía Hospital, University of Córdoba, CIBERONC, Instituto de Salud Carlos III/ Spain, Córdoba, Spain
| | - Raquel Perez-Lopez
- Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Ana Vivancos
- Cancer Genomics Lab and Molecular Pathology Lab, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
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4
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Verdaguer H, Guardiola-Fernandez M, Mancuso FM, Acosta D, Buxó E, Hernando J, Diez M, Laquente B, Baraibar I, Ros J, Garcia A, Matito J, Martin A, Sierra A, Villacampa G, Molero C, Miquel JM, Vivancos A, Dienstmann R, Macarulla T. DNA damage repair (DDR) gene mutations (mut) are predictors of response to platinum-based chemotherapy in advanced pancreatic cancer (PC) patients (pts). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e16805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e16805 Background: Somatic DDR mut have been reported in close to 10% of PC samples. In this study we investigate their predictive value for response to platinum-based chemotherapy. Methods: Case-control study with pts deriving response to oxaliplatin-based treatment (partial or complete response at any line) [n = 30] versus no response (progression in first restaging at 1st line) [n = 18]. An in-house NGS panel test of 420 genes was performed on tumor samples. DDR mut were classified in 2 subgroups: (a) functional BRCA1, BRCA2 or PALB2; and (b) any functional DDR gene mut, including those in (a). Results: 48 pts were included, median ages was 54.5 years (30-74), 29 male, 26 were diagnosed with stage IV, 36 pts (75%) received FOLFIRINOX and 37 received platinum-based chemotherapy as 1st. line treatment. Prevalence of DDR mut are described in the table. Among responders, 3 tumors had BRCA2 mt, 3 BRCA1, 2 ATM, and 1 each with BRCA2 + MSH2, PALB2, PMS2, MUYTH, RECQL4 + MDC1. Among non-responders 1 tumor each had ATM, FANCD2 and BLM. Median progression-free survival (PFS) with oxaliplatin-based chemotherapy in pts with BRCA1, BRCA2 or PALB2 mut tumors was 21.7 months (95% CI 12.3-NA); among those with any DDR mt was 12.3 months (95% CI 9.13-NA); while in pts whose tumors had no DDR mut was 6.4 months (95% CI 3.07-13)(Log-rank P-value = 0.02 comparison subgroup [a] vs. others; P-value = 0.1 subgroup [b] vs. others). Conclusions: The subgroup of pts with PC whit tumors harboring DDR gene mut, particularly functional BRCA1, BRCA2 or PALB2, have higher response rate and longer PFS with oxaplatin-based chemotherapy. [Table: see text]
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Affiliation(s)
| | | | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Daniel Acosta
- Vall d’Hebron University Hospital Barcelona Spain y Vall d’hebron insitute of Oncology (VHIO), Barcelona, Spain
| | - Elvira Buxó
- Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Marc Diez
- Vall d´Hebron University Hospital, Barcelona, Spain
| | | | - Iosune Baraibar
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Javier Ros
- Medical Oncology Department, Vall d´Hebron University Hospital/Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Agatha Martin
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Guillermo Villacampa
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Ana Vivancos
- Cancer Genomics Lab and Molecular Pathology Lab, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
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5
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Serrano C, Vivancos A, López-Pousa A, Matito J, Mancuso FM, Valverde C, Quiroga S, Landolfi S, Castro S, Dopazo C, Sebio A, Virgili AC, Menso MM, Martín-Broto J, Sansó M, García-Valverde A, Rosell J, Fletcher JA, George S, Carles J, Arribas J. Clinical value of next generation sequencing of plasma cell-free DNA in gastrointestinal stromal tumors. BMC Cancer 2020; 20:99. [PMID: 32024476 PMCID: PMC7003348 DOI: 10.1186/s12885-020-6597-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/31/2020] [Indexed: 02/08/2023] Open
Abstract
Background Gastrointestinal stromal tumor (GIST) initiation and evolution is commonly framed by KIT/PDGFRA oncogenic activation, and in later stages by the polyclonal expansion of resistant subpopulations harboring KIT secondary mutations after the onset of imatinib resistance. Thus, circulating tumor (ct)DNA determination is expected to be an informative non-invasive dynamic biomarker in GIST patients. Methods We performed amplicon-based next-generation sequencing (NGS) across 60 clinically relevant genes in 37 plasma samples from 18 GIST patients collected prospectively. ctDNA alterations were compared with NGS of matched tumor tissue samples (obtained either simultaneously or at the time of diagnosis) and cross-validated with droplet digital PCR (ddPCR). Results We were able to identify cfDNA mutations in five out of 18 patients had detectable in at least one timepoint. Overall, NGS sensitivity for detection of cell-free (cf)DNA mutations in plasma was 28.6%, showing high concordance with ddPCR confirmation. We found that GIST had relatively low ctDNA shedding, and mutations were at low allele frequencies. ctDNA was detected only in GIST patients with advanced disease after imatinib failure, predicting tumor dynamics in serial monitoring. KIT secondary mutations were the only mechanism of resistance found across 10 imatinib-resistant GIST patients progressing to sunitinib or regorafenib. Conclusions ctDNA evaluation with amplicon-based NGS detects KIT primary and secondary mutations in metastatic GIST patients, particularly after imatinib progression. GIST exhibits low ctDNA shedding, but ctDNA monitoring, when positive, reflects tumor dynamics.
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Affiliation(s)
- César Serrano
- Medical Oncology Department, Vall d'Hebron University Hospital, P. Vall d'Hebron 119, 08035, Barcelona, Spain. .,Preclinical Research Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain.
| | - Ana Vivancos
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain.
| | | | - Judit Matito
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain
| | - Claudia Valverde
- Medical Oncology Department, Vall d'Hebron University Hospital, P. Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Sergi Quiroga
- Radiology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Stefania Landolfi
- Pathology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Sandra Castro
- Surgical Oncology Division, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Cristina Dopazo
- Surgical Oncology Division, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Ana Sebio
- Medical Oncology, Sant Pau University Hospital, Barcelona, Spain
| | - Anna C Virgili
- Medical Oncology, Sant Pau University Hospital, Barcelona, Spain
| | - María M Menso
- Radiology Department, Sant Pau University Hospital, Barcelona, Spain
| | | | - Miriam Sansó
- Cancer Genomics Group,
- Vall d'Hebron Institute of Oncology, Natzaret 115, 08035, Barcelona, Spain
| | | | - Jordi Rosell
- Preclinical Research Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Jonathan A Fletcher
- Pathology Department, Brigham and Women's Hospital/Harvard Medical School, Boston, USA
| | - Suzanne George
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Joan Carles
- Medical Oncology Department, Vall d'Hebron University Hospital, P. Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Joaquín Arribas
- Preclinical Research Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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6
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Capdevila J, Mayor R, Mancuso FM, Iglesias C, Caratù G, Matos I, Zafón C, Hernando J, Petit A, Nuciforo P, Cameselle-Teijeiro JM, Álvarez C, Recio JA, Tabernero J, Matias-Guiu X, Vivancos A, Seoane J. Early evolutionary divergence between papillary and anaplastic thyroid cancers. Ann Oncol 2019; 29:1454-1460. [PMID: 29648575 DOI: 10.1093/annonc/mdy123] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Papillary thyroid cancer (PTC) is the most common thyroid carcinoma and exhibits an almost uniformly good prognosis, while anaplastic thyroid cancer (ATC) is less frequent and is one of the most aggressive cancers usually resistant to conventional treatment. Current hypothesis posits that ATC derives from PTC through the progressive acquisition of a discrete number of genomic alterations and implies that the mutational landscape of ATC resembles that of PTC. However, the clinical behaviour of ATC and PTC is radically different. We decided to address the disconnection between the clinical behaviour of ATC and PTC and the proposed model of the progressive development of ATC from PTC. Patients and methods We carried out exome sequencing of DNA from 14 ATC specimens including three cases of concomitant ATC and PTC as well as their corresponding normal DNA from 14 patients. The sequencing results were validated using droplet digital PCR. We carried out immunohistochemistry and immunofluorescence studies of the concomitant ATC and PTC cases. In addition, we integrated our sequencing results with the existing TCGA data. Results Most of the somatic mutations identified in the ATC component differed from the ones in PTC in the cases of concomitant ATC and PTC. The trunks of the phylogenetic trees representing the somatic mutations were short with long branches. In one case of concomitant PTC and ATC specimens, we observed an infiltration of PTC cells within the ATC component. Moreover, we integrated our results with data obtained from TCGA and observed that the most frequent mutations found in ATC presented high cancer cell fraction values and were significantly different from the PTC ones. Conclusion ATC diverge from PTC early in tumour development and both tumour types evolve independently. Our work allows the understanding of the relationship between ATC and PTC facilitating the clinical management of these malignancies.
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Affiliation(s)
- J Capdevila
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - R Mayor
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - F M Mancuso
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - C Iglesias
- Vall d Hebron Institute of Research (VHIR), Vall d'Hebron University Hospital, Barcelona
| | - G Caratù
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - I Matos
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - C Zafón
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - J Hernando
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - A Petit
- IDIBELL, Department of Pathology, Hospital Universitari de Bellvitge Universidad de Barcelona, Barcelona
| | - P Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona
| | - J M Cameselle-Teijeiro
- Clinical University Hospital, University of Santiago de Compostela, Santiago de Compostela
| | - C Álvarez
- Clinical University Hospital, University of Santiago de Compostela, Santiago de Compostela
| | - J A Recio
- Vall d Hebron Institute of Research (VHIR), Vall d'Hebron University Hospital, Barcelona
| | - J Tabernero
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona; CIBERONC, Barcelona; Universitat Autònoma de Barcelona, Cerdanyola del Vallès
| | - X Matias-Guiu
- IDIBELL, Department of Pathology, Hospital Universitari de Bellvitge Universidad de Barcelona, Barcelona; CIBERONC, Barcelona; Department of Pathology, Hospital Universitari Arnau de Vilanova de Lleida University of Lleida, IRBLleida, Lleida
| | - A Vivancos
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona.
| | - J Seoane
- Vall d'Hebron Institute of Oncology (VHIO) Vall d'Hebron University Hospital, Barcelona; CIBERONC, Barcelona; Universitat Autònoma de Barcelona, Cerdanyola del Vallès; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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7
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Capdevila J, Mayor R, Mancuso FM, Iglesias C, Caratú G, Matos I, Zafón C, Hernando J, Petit A, Nuciforo P, Cameselle-Teijeiro JM, Álvarez CV, Recio JA, Tabernero J, Matias-Guiu X, Vivancos A, Seoane J. Early evolutionary divergence between papillary and anaplastic thyroid cancers. Ann Oncol 2019; 30:1843. [PMID: 31406995 DOI: 10.1093/annonc/mdz216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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8
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Capdevila J, Arqués O, Hernández Mora JR, Matito J, Caratù G, Mancuso FM, Landolfi S, Barriuso J, Jimenez-Fonseca P, Lopez Lopez C, Garcia-Carbonero R, Hernando J, Matos I, Paolo N, Hernández-Losa J, Esteller M, Martínez-Cardús A, Tabernero J, Vivancos A, Palmer HG. Epigenetic EGFR Gene Repression Confers Sensitivity to Therapeutic BRAFV600E Blockade in Colon Neuroendocrine Carcinomas. Clin Cancer Res 2019; 26:902-909. [DOI: 10.1158/1078-0432.ccr-19-1266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022]
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9
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Capdevila J, Matos I, Mancuso FM, Iglesias C, Nuciforo P, Zafon C, Palmer HG, Ogbah Z, Muiños L, Hernando J, Villacampa G, Peña CE, Tabernero J, Brose MS, Schlumberger M, Vivancos A. Identification of Expression Profiles Defining Distinct Prognostic Subsets of Radioactive-Iodine Refractory Differentiated Thyroid Cancer from the DECISION Trial. Mol Cancer Ther 2019; 19:312-317. [PMID: 31540966 DOI: 10.1158/1535-7163.mct-19-0211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/17/2019] [Accepted: 09/13/2019] [Indexed: 11/16/2022]
Abstract
Several biomarkers have been suggested to have prognostic value in differentiated thyroid carcinomas (DTC) with no validation in the refractory setting, including all tumor subtypes. We aim to correlate RNA expression profiles with survival based on patients included in the DECISION trial. We obtained 247 samples from the 417 patients included in the DECISION study and performed RNAseq analysis (77 million paired-end reads for each sample on HiSeq2000). After quality control, 125 samples were included in the secondary analysis and mapped against the human reference genome (GRCh38) with STAR (v2.5.1b) using ENCODE parameter. Survival analysis was calculated using the Kaplan-Meier method and log-rank test was used for statistical comparison. In this post hoc analysis, we identified three groups of tumors based on their gene expression profile: BRAF-like, RAS-like, and non-BRAF-non-RAS-like (NoBRaL). No significant correlation with sorafenib responders was observed. However, we identified a statistically significant correlation between the RNA-expression profiles and progression-free survival. The BRAF-like profile had a significantly better outcome compared with RAS-like and NoBRaL (11.8, 6.2, and 5.5 months, respectively) [HR: 0.31, 95% confidence interval (CI), 0.17-0.60; P < 0.001 and HR: 0.36 (95% CI, 0.21-0.63); P < 0.001] and HR: 0.36 (95% CI, 0.21-0.63; P < 0.001) and maintained significance as an independent prognostic factor for overall survival in the multivariate analysis for papillary thyroid cancers. To our knowledge, this is the first comprehensive RNA-seq analysis of all histologic subtypes of DTC. The RNA expression profiles identified may suggest a new prognostic parameter to be considered before recommendation of systemic therapies or the design of stratification factors for future clinical trials.
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Affiliation(s)
- Jaume Capdevila
- Department of Medical Oncology, Vall Hebron University Hospital, Vall Hebron Institute of Oncology (VHIO), Autonomous University of Barcelona (UAB), Barcelona, Spain.
| | - Ignacio Matos
- Department of Medical Oncology, Vall Hebron University Hospital, Vall Hebron Institute of Oncology (VHIO), Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomic Group, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Carmela Iglesias
- Department of Pathology, Vall Hebron University Hospital, Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Carles Zafon
- Diabetes and Metabolism Research Unit (VHIR) and Department of Endocrinology, Vall Hebron University Hospital and Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Hector G Palmer
- Stem Cells and Cancer Group, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Zighereda Ogbah
- Cancer Genomic Group, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Muiños
- Cancer Genomic Group, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jorge Hernando
- Department of Medical Oncology, Vall Hebron University Hospital, Vall Hebron Institute of Oncology (VHIO), Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Guillermo Villacampa
- Oncology Data Science Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Carol E Peña
- Bayer HealthCare Pharmaceuticals Inc., Whippany, New Jersey
| | - Josep Tabernero
- Department of Medical Oncology, Vall Hebron University Hospital, Vall Hebron Institute of Oncology (VHIO), Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Marcia S Brose
- Department of Otorhinolaryngology, Head and Neck Surgery, and Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Ana Vivancos
- Cancer Genomic Group, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
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10
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Felip E, Navarro A, Callejo A, Martinez Marti A, Cedres S, Pardo N, Ros J, Assaf JD, Pedrola A, Viaplana C, Sansano I, Jimenez J, Nuciforo P, Sansó M, Dienstmann R, Amat R, Mancuso FM, Vivancos A. Whole exome sequencing (WES) of non-small cell lung cancer (NSCLC) for tumor mutational burden (TMB) analysis and long-term benefit to immune checkpoint inhibitors (ICIs). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.9071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9071 Background: ICIs have significantly changed the therapeutic landscape of advanced NSCLC. As such, characterizing predictive markers of long-term clinical benefit is a critical objective. TMB quantification using targeted gene panels associates with long-term response to ICIs in NSCLC patients (Rizvi H ASCO 18). Although TMB quantified by targeted NGS correlates with that of WES, caution may be needed when using smaller panels. Methods: Here we analyzed WES of tumors and matched normal tissue from 67 NSCLC patients including 42 treated with ICIs. We correlated TMB with clinico-pathological features and outcomes. TMB was categorized as high vs. low according to the upper quartile of cohort distribution. Results: The median TMB was 2.68 non-synonymous variants (nSNVs)/Mb, ranging from 0 to 15.6 nSNVs/Mb, with upper quartile at 5.42 nSNVs/Mb. TMB was higher for smoker/current smoker (median 3.51) compared to never smokers (median 0.94, p = 0.0048) but no differences were seen in elderly ( > 70 years) vs. young patients or across histologies (squamous, adeno and other) and stages at diagnosis. In patients treated with ICIs, median TMB was 5.44 for those achieving complete response, 3.87 for patients with partial response and 2.42 for patients with progressive disease (PD) (p = 0.04). Moreover, improved clinical outcomes were associated with higher TMB (Table). In patients treated with ICIs, TMB as continuous variable had an impact on progression free survival (PFS) (p = 0.03). Median PFS was 22.3 months (mo) (14-not reached) for those with high TMB and 6.4 mo (3-16) for those with low TMB (HR 0.34, 0.13-0.9, p = 0.03). Median overall survival was not reached for those patients with high TMB and 32 mo (22-43) for those with low TMB (HR 0.29, 0.1-0.86, p = 0.02). Conclusions: High TMB correlates with long-term ICI benefit in NSCLC patients. Mutations in individual genes potentially linked to long-term benefit or resistance to ICIs will be presented. [Table: see text]
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Affiliation(s)
- Enriqueta Felip
- Vall d’Hebron University Hospital, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Alejandro Navarro
- Vall d'Hebron University Hospital/Vall d´Hebron Institute Oncolgy (VHIO), Barcelona, Spain
| | - Ana Callejo
- Vall d´Hebron University Hospital /Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Alex Martinez Marti
- Vall d´Hebron University Hospital /Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Susana Cedres
- Vall d´Hebron University Hospital /Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Nuria Pardo
- Vall d’Hebron University Hospital /Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Javier Ros
- Vall D´Hebron University Hospital, Barcelona, Spain
| | | | - Anna Pedrola
- Oncology Data Science Group, Vall D’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Viaplana
- Oncology Data Science (ODysSey) Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Jose Jimenez
- Molecular Pathology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Miriam Sansó
- Cancer Genomics Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ramon Amat
- Thoracic Cancer Group, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Lab and Molecular Pathology Lab, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
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11
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Oliveira M, Ruiz-Pace F, Matito J, Perez-Lopez R, Suñol A, Bellet M, Escriva-de-Romani S, Zamora E, Gomez P, Garrigós L, Capelán M, Arumí M, Ortiz C, Amair-Pinedo F, Mancuso FM, Espinosa-Bravo M, Nuciforo P, Dienstmann R, Vivancos A, Saura C. Determinants of concordance in clinically relevant genes (CRG) from synchronously acquired tumor biopsies (tBx) and ctDNA in metastatic breast cancer (MBC). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.1075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1075 Background: NGS in ctDNA from MBC is feasible and results may be informative for patients’ management, especially in non-luminal tumors (Oliveira et al, ASCO 2018). We aimed to study the determinants of concordance in CRG in a cohort of 60 MBC patients undergoing tBx and ctDNA collection. Methods: MiSeq Amplicon-based NGS (59 cancer-related genes) was performed in one single metastatic lesion per patient and compared with liquid biopsies taken at the same time point at disease progression to prior treatment. The concordance in CRG ( PIK3CA, AKT1, ERBB2, ESR1, PTEN, BRAF, FGFR1, HRAS, KRAS, and PIK3R1) in tBx vs ctDNA was determined at patient and at mutation (mut) level and correlated with mutant allele fraction (MAF), total disease volume (TDV), and clinical characteristics. True positive in plasma (TPP): patient with a mut detected both in ctDNA and tBx. TDV was defined as all metastasis volume assessed by CT scan (excluding sclerotic bone metastasis), and analyzed by an experienced radiologist using the 3DSlicer semiautomatic segmentation tool (TDV = pixel size x number of pixels). Results: Concordance in CRG at patient and mut level was 72% and 55%, respectively. Concordance for ERBB2 (1/1; 100%) and PIK3CA (17/22; 77%) was higher than for ESR1 (8/20; 40%) and AKT1 (2/6; 33%). ctDNA failed to detect 14 mut present in tBx ( ESR1 n = 5, PIK3CA n = 5, AKT1 n = 3, BRAF n = 1). Concordance was 100% for non-luminal and 60% for luminal cases (P = 0.01). In univariate analysis, concordance was not associated with MAF in tBx (P = 0.15), TDV (p = 0.86), number of prior lines of therapy (P = 0.57), number of metastatic sites (P = 0.56) or presence of visceral metastasis (P = 1.0). In patients with PIK3CA mut (N = 22), those with TPP had a numerically higher TDV than those where a PIK3CA mut was not detected in ctDNA (20.9cm3 vs 5.1cm3, P = 0.28). Across all patients, in the multivariate logistic model adjusted for other factors, TDV was a determinant of TPP (OR 1.02, 95%CI 1.0-1.06; P = 0.059). For each increase of 1cm3 in TDV, there was a 2% increase in the probability of detecting a mut in ctDNA. Conclusions: Our results suggest that liquid biopsy testing for the detection of actionable CRG is clinically valid in MBC, although its yield depends on several factors – tumor subtype, analyzed gene, and possibly tumor volume – that reflect both tumor heterogeneity and tumor shedding rate. Due to the potential clinical implications, the observation that mutation detection in ctDNA may correlate with tumor volume merits further study in a larger dataset.
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Affiliation(s)
- Mafalda Oliveira
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Fiorella Ruiz-Pace
- Oncology Data Science (ODysSey) Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Raquel Perez-Lopez
- Radiomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Anna Suñol
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Meritxell Bellet
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Santiago Escriva-de-Romani
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Esther Zamora
- Medical Oncology Department, Vall d'Hebron University Hospital. Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Patricia Gomez
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laia Garrigós
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Capelán
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Miriam Arumí
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Carolina Ortiz
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Fabiola Amair-Pinedo
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Martin Espinosa-Bravo
- Breast Surgical Unit, Breast Cancer Center, Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Lab and Molecular Pathology Lab, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Saura
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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12
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Oliveira M, Bellet M, Suñol A, Ruiz-Pace F, Gomez P, Escrivá S, Garrigós L, Zamora E, Capelán M, Azaro A, Arumí M, Ortiz C, Matito J, Fasani R, Mancuso FM, Espinosa M, Nuciforo P, Dienstmann R, Vivancos A, Saura C. Concordance of genomic alterations (GA) in synchronous tumor biopsies (tBx) and circulating tumor (ct) DNA from metastatic breast cancer (MBC) patients (pts). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.1073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mafalda Oliveira
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Meritxell Bellet
- Vall d'Hebron University Hospital and Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Anna Suñol
- Breast Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Fiorella Ruiz-Pace
- Oncology Data Science (ODysSey) Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Patricia Gomez
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Santiago Escrivá
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laia Garrigós
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Esther Zamora
- Medical Oncology Department, Vall d'Hebron University Hospital. Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Capelán
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Analía Azaro
- Medical Oncology Department, Vall d’Hebron University Hospital; Molecular Therapeutics Research Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Miriam Arumí
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Carolina Ortiz
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Roberta Fasani
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Martin Espinosa
- Breast Surgical Unit, Breast Cancer Center, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science (ODysSey) Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Saura
- Medical Oncology Department, Breast Cancer Group, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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13
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Capdevila J, Matos Garcia I, Mancuso FM, Iglesias C, Nuciforo P, Zafon C, Palmer HG, Ogbah Z, Muiños L, Pena CE, Brose MS, Schlumberger M, Vivancos A. RNAseq analysis of the sorafenib phase III DECISION trial in differentiated thyroid cancer (DTC): Correlation with clinical outcome. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.6083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
6083 Background: In DECISION, sorafenib significantly impacted progression-free survival (PFS) and response rate (RR) in radioactive-iodine refractory DTC. The aim of this biomarker study was to identify RNA expression profiles related with PFS, overall survival (OS) and RR and to describe the expression profiles of DTC histologies. Methods: Of the 417 patients in the trial, 247 had sufficient formalin fixed paraffin embedded archival tumor material for RNAseq. We generated on average 77 million paired-end reads for each sample on HiSeq2000 (Illumina). RNAseq reads were mapped against the human reference genome (GRCh38) with STAR (v2.5.1b) using ENCODE parameters. 125 samples had sufficient quality to be included in the analysis. Results: The analysis subset included 68 sorafenib and 57 placebo patients (PFS 10.3 vs 7.4 months, HR: 0.62 CI 95% 0.38-0.99, p = 0.046). Unsupervised clustering using the 100 most variable genes identified 3 groups: BRAF-like (included most of the BRAF-mutated tumors), RAS-like (included most of the RAS mutated tumors) and non-BRAF-non-RAS-like group (included most wild-type tumors). These groups, based on the mutational profile, can be correlated with tumor type: the papillary BRAF-mutant, the follicular wild-type, and a third group with papillary, follicular and poorly differentiated with predominant RAS mutations. A Student t-test comparing papillary and follicular histologies revealed a signature of 283 genes with significantly different expression that, within the papillary tumors, identifies a subset with an expression profile more similar to follicular. No RNA signatures correlating with benefit from sorafenib were identified. Conclusions: While papillary and follicular thyroid cancers have significantly different RNA expression profiles, a subset of papillary has been identified with an expression profile more similar to follicular. In addition, a unified RAS-like expression profile spans subsets of papillary, follicular, and poorly differentiated thyroid cancers, suggesting that tumor biology can be similar across histologies. Clinical trial information: NCT00984282.
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Affiliation(s)
- Jaume Capdevila
- Vall d’Hebron University Hospital Institute of Oncology (VHIO), Barcelona, Spain
| | - Ignacio Matos Garcia
- Vall d’Hebron University Hospital Institute of Oncology (VHIO), Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Carmela Iglesias
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Carles Zafon
- Department of Endocrinology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Hector G. Palmer
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Laura Muiños
- Vall d’Hebron University Hospital Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Marcia S. Brose
- Department of Otorhinolaryngology: Head and Neck Surgery, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA
| | | | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
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14
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Vivancos A, Palmer HG, Ogbah Z, Matito J, Mancuso FM, Navarro A, Martinez Marti A, Argiles G, Elez E, Rodón J, Nuciforo P, Tabernero J, Felip E. Analysis of RSPO gene expression in solid tumors. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Hector G. Palmer
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Alejandro Navarro
- Medical Oncology Department Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Alex Martinez Marti
- Medical Oncology Department Vall d´Hebron Institute of Oncology-Vall D'Hebron University Hospital, Barcelona, Spain
| | | | - Elena Elez
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Jordi Rodón
- Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology, Barcelona, Spain, Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Pathology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
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15
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Engelken J, Espadas G, Mancuso FM, Bonet N, Scherr AL, Jímenez-Álvarez V, Codina-Solà M, Medina-Stacey D, Spataro N, Stoneking M, Calafell F, Sabidó E, Bosch E. Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver. Mol Biol Evol 2016; 33:738-54. [PMID: 26582562 PMCID: PMC4760079 DOI: 10.1093/molbev/msv267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients.
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Affiliation(s)
- Johannes Engelken
- †These authors contributed equally to this work. ‡Deceased October 23, 2015. Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guadalupe Espadas
- †These authors contributed equally to this work. Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesco M Mancuso
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Bonet
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
| | - Anna-Lena Scherr
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Victoria Jímenez-Álvarez
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Codina-Solà
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniel Medina-Stacey
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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16
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Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L. Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome. Proteomics 2015; 16:554-63. [PMID: 26702875 DOI: 10.1002/pmic.201500187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 11/06/2015] [Accepted: 12/21/2015] [Indexed: 02/05/2023]
Abstract
A common problem encountered when performing large-scale MS proteome analysis is the loss of information due to the high percentage of unassigned spectra. To determine the causes behind this loss we have analyzed the proteome of one of the smallest living bacteria that can be grown axenically, Mycoplasma pneumoniae (729 ORFs). The proteome of M. pneumoniae cells, grown in defined media, was analyzed by MS. An initial search with both Mascot and a species-specific NCBInr database with common contaminants (NCBImpn), resulted in around 79% of the acquired spectra not having an assignment. The percentage of non-assigned spectra was reduced to 27% after re-analysis of the data with the PEAKS software, thereby increasing the proteome coverage of M. pneumoniae from the initial 60% to over 76%. Nonetheless, 33,413 spectra with assigned amino acid sequences could not be mapped to any NCBInr database protein sequence. Approximately, 1% of these unassigned peptides corresponded to PTMs and 4% to M. pneumoniae protein variants (deamidation and translation inaccuracies). The most abundant peptide sequence variants (Phe-Tyr and Ala-Ser) could be explained by alterations in the editing capacity of the corresponding tRNA synthases. About another 1% of the peptides not associated to any protein had repetitions of the same aromatic/hydrophobic amino acid at the N-terminus, or had Arg/Lys at the C-terminus. Thus, in a model system, we have maximized the number of assigned spectra to 73% (51,453 out of the 70,040 initial acquired spectra). All MS data have been deposited in the ProteomeXchange with identifier PXD002779 (http://proteomecentral.proteomexchange.org/dataset/PXD002779).
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Affiliation(s)
- Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco M Mancuso
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Proteomics Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Héctor Climente-González
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marcia I Peña-Paz
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Proteomics Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Eduard Sabido
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Proteomics Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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17
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Baumstark R, Hänzelmann S, Tsuru S, Schaerli Y, Francesconi M, Mancuso FM, Castelo R, Isalan M. The propagation of perturbations in rewired bacterial gene networks. Nat Commun 2015; 6:10105. [PMID: 26670742 DOI: 10.1038/ncomms10105] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/04/2015] [Indexed: 11/09/2022] Open
Abstract
What happens to gene expression when you add new links to a gene regulatory network? To answer this question, we profile 85 network rewirings in E. coli. Here we report that concerted patterns of differential expression propagate from reconnected hub genes. The rewirings link promoter regions to different transcription factor and σ-factor genes, resulting in perturbations that span four orders of magnitude, changing up to ∼ 70% of the transcriptome. Importantly, factor connectivity and promoter activity both associate with perturbation size. Perturbations from related rewirings have more similar transcription profiles and a statistical analysis reveals ∼ 20 underlying states of the system, associating particular gene groups with rewiring constructs. We examine two large clusters (ribosomal and flagellar genes) in detail. These represent alternative global outcomes from different rewirings because of antagonism between these major cell states. This data set of systematically related perturbations enables reverse engineering and discovery of underlying network interactions.
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Affiliation(s)
- Rebecca Baumstark
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Sonja Hänzelmann
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Saburo Tsuru
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yolanda Schaerli
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Mirko Francesconi
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Francesco M Mancuso
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Genomics Cancer Group, Vall d 'Hebron Institute of Oncology (VHIO), Carrer Natzaret 15-17, 08035 Barcelona, Spain
| | - Robert Castelo
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dr Aiguader 88, 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Mark Isalan
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain.,Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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18
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Mihailovich M, Bremang M, Spadotto V, Musiani D, Vitale E, Varano G, Zambelli F, Mancuso FM, Cairns DA, Pavesi G, Casola S, Bonaldi T. miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nat Commun 2015; 6:8725. [PMID: 26555894 PMCID: PMC4667639 DOI: 10.1038/ncomms9725] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/22/2015] [Indexed: 01/07/2023] Open
Abstract
The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 3′ untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c-MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 3′ UTR shortening at different stages of tumorigenesis. The synergism between c-MYC and miR-17-19b plays an important role in lymphoma initiation. In this study, the authors identify a panel of targets co-regulated by miR-17-19b and in MYC-driven lymphoma and unravel the molecular mechanism through which miR-17-19b inhibits MYC translation.
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Affiliation(s)
- Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Valeria Spadotto
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Daniele Musiani
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Elena Vitale
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Gabriele Varano
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | | | - Francesco M Mancuso
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - David A Cairns
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Giulio Pavesi
- Department of Biosciences, Milan University, Milan 20133, Italy
| | - Stefano Casola
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
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19
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Capdevila J, Vivancos A, Matias-Guiu X, Iglesias C, Salva F, Serres X, Gonzalez O, Caubet E, Jimenez J, Zafon C, Mancuso FM, Caratu G, Alvarez C, Mayor R, Tabernero J, Seoane J. Genomic landscape of anaplastic thyroid cancer. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.6033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | - Carmela Iglesias
- Department of Pathology. Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Salva
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Xavier Serres
- Department of Radiology. Vall d'Hebron University Hospital, Barcelona, Spain
| | - Oscar Gonzalez
- Department of Surgery, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Enric Caubet
- Department of Surgery, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Jose Jimenez
- Molecular Pathology Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Carles Zafon
- Department of Endocrinology. Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Ginevra Caratu
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Clara Alvarez
- Santiago de Compostela University, Santiago De Compostela, Spain
| | - Regina Mayor
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Joan Seoane
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
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20
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Ortiz C, Argilés G, Élez E, Matito J, Mendizabal L, Lo Giacco D, Mancuso FM, Sanz-Garcia E, Macarulla T, Alsina M, Capdevila J, Saurí T, Azaro A, Cruz C, Hierro C, Ramon y Cajal S, Nuciforo P, Rodón J, Tabernero J, Vivancos A. Measuring the impact of Next Generation Sequencing (NGS) technique implementation in metastatic colorectal cancer (mCRC) drug development program. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.3598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Elena Élez
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Leire Mendizabal
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Deborah Lo Giacco
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Francesco M Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | | | - Maria Alsina
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | - Tamara Saurí
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Analia Azaro
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Cristina Cruz
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Cinta Hierro
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | - Paolo Nuciforo
- Molecular Pathology Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Jordi Rodón
- Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | | | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
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21
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Casas C, Isus L, Herrando-Grabulosa M, Mancuso FM, Borrás E, Sabidó E, Forés J, Aloy P. Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage. Sci Rep 2015; 5:9185. [PMID: 25784190 PMCID: PMC5378195 DOI: 10.1038/srep09185] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 02/05/2015] [Indexed: 12/14/2022] Open
Abstract
Neurodegenerative processes are preceded by neuronal dysfunction and synaptic disconnection. Disconnection between spinal motoneuron (MN) soma and synaptic target leads either to a retrograde degenerative process or to a regenerative reaction, depending injury proximity among other factors. Distinguished key events associated with one or other processes may give some clues towards new therapeutical approaches based on boosting endogenous neuroprotective mechanisms. Root mechanical traction leads to retrograde MN degeneration, but share common initial molecular mechanisms with a regenerative process triggered by distal axotomy and suture. By 7 days post-injury, key molecular events starts to diverge and sign apart each destiny. We used comparative unbiased proteomics to define these signatures, coupled to a novel network-based analysis to get biological meaning. The procedure implicated the previous generation of combined topological information from manual curated 19 associated biological processes to be contrasted with the proteomic list using gene enrichment analysis tools. The novel and unexpected results suggested that motoneurodegeneration is better explained mainly by the concomitant triggering of anoikis, anti-apoptotic and neuropathic-pain related programs. In contrast, the endogenous neuroprotective mechanisms engaged after distal axotomy included specifically rather anti-anoikis and selective autophagy. Validated protein-nodes and processes are highlighted across discussion.
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Affiliation(s)
- Caty Casas
- Group of Neuroplasticity and Regeneration, Institut de Neurociències and Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, and Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 08193 Bellaterra, Barcelona, Spain
| | - Laura Isus
- Joint IRB-BSC-CRG Program in Computational Biology. Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Catalonia, Spain
| | - Mireia Herrando-Grabulosa
- Group of Neuroplasticity and Regeneration, Institut de Neurociències and Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, and Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 08193 Bellaterra, Barcelona, Spain
| | - Francesco M. Mancuso
- Proteomic Unit, Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eva Borrás
- Proteomic Unit, Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduardo Sabidó
- Proteomic Unit, Centre for Genomic Regulation (CRG) and UPF, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Joaquim Forés
- Hand and Peripheral Nerve Unit, Hospital Clínic i Provincial, Universitat de Barcelona, Barcelona, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology. Institute for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
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22
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Meijer HJG, Mancuso FM, Espadas G, Seidl MF, Chiva C, Govers F, Sabidó E. Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans. Mol Cell Proteomics 2014; 13:2101-13. [PMID: 24872595 PMCID: PMC4125740 DOI: 10.1074/mcp.m113.035873] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 05/09/2014] [Indexed: 11/06/2022] Open
Abstract
Oomycetes are filamentous organisms that cause notorious diseases, several of which have a high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes, and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focused on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyze P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses, and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.
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Affiliation(s)
- Harold J G Meijer
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Francesco M Mancuso
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guadalupe Espadas
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael F Seidl
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; ‖Centre for BioSystems Genomics, Droevendaalsesteeg, 16708 PB Wageningen, The Netherlands
| | - Cristina Chiva
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Francine Govers
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; ‖Centre for BioSystems Genomics, Droevendaalsesteeg, 16708 PB Wageningen, The Netherlands
| | - Eduard Sabidó
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain;
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Ferreira R, Vitorino R, Padrão AI, Espadas G, Mancuso FM, Moreira-Gonçalves D, Castro-Sousa G, Henriques-Coelho T, Oliveira PA, Barros AS, Duarte JA, Sabidó E, Amado F. Lifelong exercise training modulates cardiac mitochondrial phosphoproteome in rats. J Proteome Res 2014; 13:2045-55. [PMID: 24467267 DOI: 10.1021/pr4011926] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Moderate physical activity has traditionally been associated with the improvement of cardiac function and, consequently, with the extension of life span. Mitochondria play a key role in the adaptation of heart muscle to exercise-related metabolic demands. In order to disclose the molecular mechanisms underlying the beneficial effect of lifelong physical activity in cardiac function, we performed label-free quantitative mass spectrometry-based proteomics of Sprague-Dawley rat heart mitochondrial proteome and phosphoproteome. Our data revealed that 54 weeks of moderate treadmill exercise modulates the abundance of proteins involved in the generation of precursor metabolites and cellular respiration, suggesting an increase in carbohydrate oxidation-based metabolism. Moreover, from the 1335 phosphopeptides identified in this study, 6 phosphosites were exclusively assigned to heart mitochondria from sedentary rats and 17 to exercised animals, corresponding to 6 and 16 proteins, respectively. Most proteins exhibiting significant alterations in specific phosphorylation sites were involved in metabolism. Analysis of the acquired data led to the identification of several kinases potentially modulated by exercise training, which were selected for further validation. Indeed, higher protein abundance levels of RAF and p38 in mitochondria were confirmed to be modulated by sustained exercise. Our work describes the plasticity of heart mitochondria in response to long exercise programs manifested by the reprogramming of phosphoproteome and provides evidence for the kinases involved in the regulation of metabolic pathways and mitochondrial maintenance.
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Affiliation(s)
- Rita Ferreira
- QOPNA, Department of Chemistry and ¶School of Health Sciences, University of Aveiro , Aveiro 3810-193, Portugal
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Borràs E, Espadas G, Mancuso FM, Maier T, Chiva C, Sabidó E. Integrative quantitation enables a comprehensive proteome comparison of two Mycoplasma pneumoniae genetic perturbations. Mol BioSyst 2013; 9:1249-56. [DOI: 10.1039/c3mb25581f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mihailovich M, Wurth L, Zambelli F, Abaza I, Militti C, Mancuso FM, Roma G, Pavesi G, Gebauer F. Widespread generation of alternative UTRs contributes to sex-specific RNA binding by UNR. RNA 2012; 18:53-64. [PMID: 22101243 PMCID: PMC3261744 DOI: 10.1261/rna.029603.111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Accepted: 10/03/2011] [Indexed: 05/31/2023]
Abstract
Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to msl2 mRNA and the noncoding RNA roX is believed to play key roles in the control of X-chromosome dosage compensation in both sexes. To investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of noncoding RNAs in a sex-specific fashion. The analyses also reveal a strong correlation between sex-specific binding of UNR and sex-specific differential expression of UTRs in target genes. Validation experiments indicate that UNR indeed recognizes sex-specifically processed transcripts. These results suggest that UNR exploits the transcript diversity generated by alternative processing and alternative promoter usage to bind and regulate target genes in a sex-specific manner.
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Affiliation(s)
- Marija Mihailovich
- Gene Regulation Programme, Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
| | - Laurence Wurth
- Gene Regulation Programme, Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
| | - Federico Zambelli
- Department of Biomolecular Science and Biotechnology, University of Milano, 20133 Milano, Italy
| | - Irina Abaza
- Gene Regulation Programme, Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
| | - Cristina Militti
- Gene Regulation Programme, Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
| | - Francesco M. Mancuso
- Bioinformatics Unit, Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
| | - Guglielmo Roma
- Bioinformatics Unit, Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
| | - Giulio Pavesi
- Department of Biomolecular Science and Biotechnology, University of Milano, 20133 Milano, Italy
| | - Fátima Gebauer
- Gene Regulation Programme, Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Spain
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Mancuso FM, Montfort M, Carreras A, Alibés A, Roma G. HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data. BMC Res Notes 2011; 4:546. [PMID: 22182516 PMCID: PMC3285701 DOI: 10.1186/1756-0500-4-546] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 12/19/2011] [Indexed: 01/16/2023] Open
Abstract
Background The study of the human DNA methylome has gained particular interest in the last few years. Researchers can nowadays investigate the potential role of DNA methylation in common disorders by taking advantage of new high-throughput technologies. Among these, Illumina Infinium assays can interrogate the methylation levels of hundreds of thousands of CpG sites, offering an ideal solution for genome-wide methylation profiling. However, like for other high-throughput technologies, the main bottleneck remains at the stage of data analysis rather than data production. Findings We have developed HumMeth27QCReport, an R package devoted to researchers wanting to quickly analyse their Illumina Infinium methylation arrays. This package automates quality control steps by generating a report including sample-independent and sample-dependent quality plots, and performs primary analysis of raw methylation calls by computing data normalization, statistics, and sample similarities. This package is available at CRAN repository, and can be integrated in any Galaxy instance through the implementation of ad-hoc scripts accessible at Galaxy Tool Shed. Conclusions Our package provides users of the Illumina Infinium Methylation assays with a simplified, automated, open-source quality control and primary analysis of their methylation data. Moreover, to enhance its use by experimental researchers, the tool is being distributed along with the scripts necessary for its implementation in the Galaxy workbench. Finally, although it was originally developed for HumanMethylation27, we proved its compatibility with data generated with the HumanMethylation450 Bead Chip.
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Affiliation(s)
- Francesco M Mancuso
- Bioinformatics Unit, Centre for Genomic Regulation (CRG) and UPF, Dr, Aiguader 88, 08003 Barcelona, Spain.
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Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Grianti P, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS Biol 2011; 9:e1001086. [PMID: 21738444 PMCID: PMC3125158 DOI: 10.1371/journal.pbio.1001086] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 05/05/2011] [Indexed: 11/18/2022] Open
Abstract
The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation.
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Affiliation(s)
| | - Assaf Weiner
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Francesca Di Felice
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | | | - Elisa Cesarini
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Riccardo L. Rossi
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | - Lorna Gregory
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dilair Baban
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Grazisa Rossetti
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | - Paolo Grianti
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Pagani
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | | | - Jiannis Ragoussis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nir Friedman
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
| | - Marco E. Bianchi
- San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy
- * E-mail: (MEB); (AA)
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy
- * E-mail: (MEB); (AA)
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Mancuso FM. Codependency in nursing students: recognition and modification of behavioral characteristics. Nursingconnections 1999; 11:55-60. [PMID: 9883182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Recent literature estimates that there are approximately 2 1/2 million nurses; of these a significant number may exhibit signs of codependency, a behavior pattern that impedes an individual's ability to relate to others on mature level. Codependency develops in dysfunctional family systems and manifests itself in compulsive behaviors that make life painful and work emotionally difficult. Often, constructive communication is difficult as codependent persons tend to feel low self-esteem and low self-worth. Nursing students may exhibit characteristic codependency traits among fellow students in the classroom, in the clinical setting, and in interactions with faculty. Nurse educators, through their own self-awareness, introspection, and knowledge of the behaviors and characteristics of codependency, can facilitate more effective communication with all nursing students to promote healthier interactions and relationships. Techniques to modify one's method of interacting with others have clear potential for improving professional as well as personal relationships.
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Faulk D, Mancuso FM. A collaborative effort for sex education in rural school settings. Nurs Health Care Perspect 1998; 19:271-3. [PMID: 10478068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Many students report that sex and sexuality education is, at best, inappropriate and, at worst, nonexistent. Alarming statistics for teen pregnancy and a high incidence of sexually transmitted diseases support the need for education and intervention targeted at a young audience. The traditional approach, to incorporate sex education into health education classes taught by schoolteachers, can be difficult to accomplish in rural school settings where adequate financial resources and community involvement are lacking. Through a partnership funded by the W. K. Kellogg Foundation, a collaborative approach was used in two rural Southeastern communities to deliver a program of sex education to students in fourth through sixth grades. The program united the efforts of community leaders, the school administration, parents, and students and faculty of a university school of nursing.
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Affiliation(s)
- D Faulk
- Auburn University Montgomery School of Nursing, Alabama, USA
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